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Daniel Dunaief

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Image from Wikimedia Commons public domain

By Daniel Dunaief

Daniel Dunaief

I watch Jeopardy! and it’s a much more intellectual and challenging show than Family Feud, but, truth be told, I have watched several episodes of the Feud these days.

Perhaps it’s the simplicity of the show that entertains me or the fact that there just doesn’t seem to be much at stake. Sometimes, the questions seem ridiculous and, somewhere among the answers, is something about someone’s private parts, poop, or people’s mothers, almost as if I’m watching a game show version of an Adam Sandler movie.

Anyway, watching the show late at night, I have started imagining a farce, skit or just a show gone awry that I would enjoy watching, particularly when I’m in that time between mental focus and drifting off into an imaginary world where I am on skis and can jump over a mountain, land in a nearby ocean, communicate with dolphins and have dinner with a coed group of mermaids who particularly enjoy conversations about science, conservation and baseball.

In my imaginary episode, Steve Harvey starts with an apology, admitting that the word “theyself” isn’t a word. Then, as he meets the families, the first person in the family introduces their relatives.

“Hi Steve, I’m Joe and this is my wife whose favorite word late at night seems to be ‘no’ and who still hasn’t figured out how to bake chicken without burning it.”

Steve widens his eyes, takes a few steps back and lowers his jaw.

“And, next to her, is my sister-in-law Erica, who always knows better about everything and clearly thought my wife could do better when we got married. I have news for you, sis. Maybe she could have, but she chose me anyway, so get over yourself and show the world how smart you are.”

A little less shocked, Steve nods, looking past the mortified sister in law.

“Oh, that’s my brother-in-law Eric. If you were named Eric, would you date a woman named Erica? Eric and I share a beer once in a while, but he frequently has bad breath, so I wouldn’t get too close to him.”

Steve turns his head and makes a mental note.

“And, down at the end, that’s a neighbor of ours, Jessica, whom we’re passing off as a member of the family because no one else in our family could stand to be with us and because they didn’t believe we’d actually be on the Feud. So, hey, to the rest of the family, suck it!”

After an introduction from the other family, the two leaders come to the front of the podium for the obligatory hand shake. Joe refuses to shake hands and suggests that he has OCD and that he’ll tap feet instead.

Looking at the card, Steve shakes his head and says the top six answers are on the board.

“Name a time when you wish you were somewhere else,” he says.

Alex buzzes in first and Joe starts screaming that he’s sure he beat Alex and demands a replay review.

“We don’t do that here,” Steve says, frowning at Joe. “Have you ever watched the show?”

“But they do it in sports. Why not? It’s unfair. Don’t I get at least one challenge? I brought my own red flag,” Joe protests.

“I don’t care what you brought,” Steve says, forcing a smile on his bewildered face. “You don’t get a challenge. Let Alex answer.”

Steve turns to Alex.

“I was going to say ‘at the dentist’ but I’m changing my answer to ‘now.’”

Steve doubles over with laughter, holding the podium and shaking his head.

“Why is that funny?” Joe demands. “Besides, I have a better answer.”

“Let’s see where ‘now’ lands on the list,” Steve says, pointing to the board. It’s the third-most popular answer, which means Joe gets to speak. Steve turns to him, waiting for a reply.

“7:57 am on most mornings,” Joe says, smiling.

Steve doesn’t dare ask, repeating Joe’s answer, which gets the familiar red X.

“But it was a great answer,” Joe demands. “Can I challenge that?”

“No, you want to play or pass?” Steve asks, turning to Alex.

After Alex’s family clears all but one answer, Steve returns to Joe.

“Okay,” Steve says, treading carefully. “Name a time when you wish you were somewhere else?”

“When we first auditioned for the show?” Joe replies.

Steve laughs, pats him on the back and wishes him well.

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METRO photo

By Daniel Dunaief

Daniel Dunaief

The number of Advanced Placement courses has expanded dramatically since parents were the age of their high school children.

Whereas we could have taken, say, four or five APs, the modern high school student can graduate with considerably more.

Current students can and sometimes do take as many as eight, nine, 10 or more AP classes, in the hopes of knocking the socks off college admissions counselors, guidance counselors and future prospective employers. All those AP classes can also give students enough college credits to help them graduate in under four years.

I’d like to propose my own list of AP classes for future generations.

— AP Listening. So many people love to talk, to hear their own voices, and to tell others how they’re wrong even before people can share a fully formed opinion. In this class, students would be required to listen to new ideas, to consider them and to react and interact with others. Speaking would be considerably less important than listening carefully.

— AP Conspiracy Theory. We all know that conspiracy theories are as ubiquitous as “Welcome” signs in corner stores. This AP class would look deeply at some of the most detailed conspiracy theories, giving students a chance to question everyone and everything, including those people who create and pass along conspiracies.

— AP Saying No. To borrow from former First Lady Nancy Reagan, saying “no” to drugs, among other things, is a healthy and important part of growing up and making the most of the college experience. The class could provide students with a wide range of situations in which students say “no” without damaging their ego or social status.

— AP Social Media Etiquette, or SME, for short. Some seniors get into colleges well before their colleagues. When they do, they post pictures of themselves on campus, their parents wearing gear from the school that admitted them, and the school emblem or insignia with confetti coming down from the top of the screen. Yes, you got into college, and yes, that’s wonderful, but other members of your class are still applying and don’t need to feel awful because they haven’t gotten in anywhere yet.

— AP It’s Not About Me (or, perhaps, INAM). Yes, this is a bit like a psychology class, but instead of studying theories and psychology legends, these students could explore real-life scenarios in which, say, Sue becomes angry with John. John may not have done anything in particular, but Sue may be reacting to someone else in her life, like her parents forcing her to take AP It’s Not About Me instead of going to soccer practice.

— AP Take Responsibility. When something goes wrong at school, work or in the house, it’s far too easy to point the finger at someone else. In this class, students can learn how to take responsibility, when it’s appropriate, and demonstrate courage, leadership, and initiative in accepting responsibility for their mistakes.

— AP Personal History. Each of us has our own story to tell. Colleges urge prospective students to find their authentic voice. That’s not always easy in a world filled with formulas and scripted and structured writing. In this personal history class, students could take a microscope to their own lives and to the lives of their extended family, understanding and exploring characteristics and life stories. Students might discover family patterns they wish to emulate or to avoid at all costs.

— AP Tail Wagging. While the world is filled with problems, students could explore modern and historical moments and ideas that inspire them and that give them reasons to celebrate. This class could blend a combination of historical triumphs with small daily reasons to celebrate or, if you prefer, to wag your tail.

— AP Get to Know Your Parents. High school students who are well ahead of their time emotionally and intellectually may come to the conclusion many others reach before their mid 20’s: that their parents are, big shock here, people! Yeah, we do ridiculous thing like send them in the wrong clothing to school, miss important dances, and embarrass them by kissing them in front of their friends. This course could help accelerate the process of seeing parents for the imperfect creatures who love them unconditionally.

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Evan Musterman with lead SRX beamline scientist Andrew Kiss at the SRX beamline. Photo by Kevin Coughlin/Brookhaven National Laboratory

By Daniel Dunaief

When he took over to lead the sub micron resolution X-ray spectroscopy, or SRX, beamline at Brookhaven National Laboratory on January 1, 2020, Andrew Kiss expected to balance between improving the machinery and helping visiting scientists use it. The pandemic, however, altered that balance.

BNL received components for the beamline in December 2019, when the researchers were going to try to take a fraction of the available x-ray time to install and commission it, all while still running experiments. The pandemic, however, kept scientists from visiting the site. That meant Kiss and his colleagues could dedicate more time to technical enhancements.

“Since the pandemic shut down the user program, this gave us an opportunity to focus all of our time on the new equipment” that visiting researchers could tap into when they returned, he explained in an email.

The beamline, which postdoctoral researcher Evan Musterman is enhancing further with diffraction techniques to reveal information about strain (see related story here), is in high demand. During the current cycle, 324 researchers applied for beamline time, while 99 time slots were allocated.

Scientists have a range of ways of discovering which beamline might best suit their research needs, including word of mouth. Kiss has had conversations with researchers who describe how they read something in a research paper and have similar goals.

Scientists “usually have a good idea of what instrument/ facility to use and why it is good for their research so informal conversations at conferences and seminars can be very useful,” Kiss said.

Most of Kiss’s time is dedicated to ensuring the stability and reliability of the beamline, as well as extending its capabilities to scan larger regions with less overhead, he explained.

“All of this is to help the researchers that come to the beamline, but my hope is that with this baseline of reliable and fast data acquisition, I can focus more on scientific topics such as metal additive manufacturing,” Kiss wrote.

With the SRX, Kiss can explore applied questions related to corrosion effects or how a material is modified by exposure to different gases, liquids or other parameters.

Working at the beamline has given Kiss an unusual perspective outside the lab. A few years ago, he received a notification about a recall on baby food he purchased that could have elevated levels of something unhealthy in it. His second thought, after making sure he didn’t give any to the child, was to wonder how much was in the food and if he could measure it. Before he could bring it to the lab, the contaminated food was already taken away with the garbage.

Kiss enjoys his work and suggested that the field attracts a “certain type of person and, once you are there, it is tough to pull yourself away from the instrument and the community of researchers around you,” he explained.

In addition to making basic discoveries in fields such as materials science, Earth science and biological sciences, the SRX beamline has played an important role in studies that have affected public policy.

Indeed, a study in 2022 showed that veterans who worked in Iraq and Afghanistan near burn pits had oxidized particles of iron and titanium in their lungs. “This is not direct evidence it came from a burn pit, but these were not seen in healthy lungs,” Kiss said. Only a few places in the world had the kind of machinery with a bright enough source and high enough resolution to discover these particles.

Kiss and collaborators from other laboratories, universities and medical institutions appreciated the opportunity to have a “positive impact on these soldiers’ lives by providing the measurements to get them help,” he said. The discovery of these elements in the lungs of veterans who lived near burn pits and suffered health consequences, which the study at SRX and other facilities helped demonstrate, led to the Pact Act, which President Joe Biden signed into law in 2022 and which provides $280 billion in federal funding for the health effects veterans suffer after exposure to such toxins.

SRX has high spatial resolution and is highly sensitive to trace concentrations for elemental mapping and chemical composition. SRX is an x-ray fluorescence microscope with “high spatial resolution and highly sensitive to trace concentrations for elemental mapping and chemical composition,” Kiss said. “If that can be used to help people’s lives, that is a wonderful thing.”

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Evan Musterman at the SRX beamline. Photo by Kevin Coughlin/Brookhaven National Laboratory

By Daniel Dunaief

It’s everywhere, from holding the water we drink to providing a cover over the Norman Rockwell painting of “The Three Umpires” to offering a translucent barrier between our frigid winter backyards and the warm living room.

While we can hold it in our hands and readily see through it, glass and its manufacture, which has been ongoing for about 4,000 years, has numerous mysteries.

Indeed, given enough temperature and time, glass crystallizes. Controlling the process has been used to increase strength and chemical durability, tailor thermal properties and more over the last several decades.

Evan Musterman, who studied the way lasers served as a localized heat source to induce single crystal formation in glass when he was a graduate student at Bethlehem, Pennsylvania-based Lehigh University, joined Brookhaven National Laboratory in September as a postdoctoral researcher.

Musterman, who received funding for nine months at the end of his PhD program through the Department of Energy’s Office of Science Graduate Student Research program when he was at Lehigh that enabled him to work at BNL, is adding scanning x-ray diffraction mapping as a more user-ready technique at the Submicron Resolution X-ray Spectroscopy beamline (or SRX) that he used as a graduate student. 

The beamline looks at x-ray fluorescence measurements, which provide information about the elemental distribution and chemical information, such as oxidation state and bond distances, in an experimental sample. The next component scientists are looking for is using diffraction to inform the crystal structure of the material and to gather information about strain, explained Andrew Kiss, the lead beamline scientist for the SRX.

Musterman hopes to build on the electron diffraction mapping he did during his PhD work when he studied the crystals he laser-fabricated in glass. X-rays, he explained, are more sensitive to atomic arrangements than electrons and are better at mapping strain.

Musterman’s “background in materials science and crystal structures made him an excellent candidate for a post-doc position,” Kiss said.

The SRX has applications in material science, geological science and biological imaging, among other disciplines. 

Glass questions

For his PhD research, Musterman worked to understand how glass is crystallizing, particularly as he applied a laser during the process. He explored how crystal growth in glass is unique compared with other methods, leading to new structures where the crystal lattice can rotate as it grows.

Musterman finds the crystallization of glass ‘fascinating.” Using diffraction, he was able to watch the dynamics of the earliest stages after a crystal has formed. In his PhD work, he used a spectroscopy method to understand the dynamics of glass structure before the crystal had formed.

Musterman started working at the SRX beamline in June of 2022. He was already familiar with the beamline operation, data collection and types of data he could acquire, which has given him a head start in terms of understanding the possibilities and limitations.

In his postdoctoral research, he is developing diffraction mapping and is also finishing up the experiments he conducted during his PhD.

Himanshu Jain, Musterman’s PhD advisor at Lehigh who is Professor of Materials Science and Engineering, was pleased with the work Musterman did during his five years in his lab. Jain sees potential future extensions and applications of those efforts.

Musterman’s research “forms a foundation for integrated photonics, which is expected to revolutionize communications, sensors, computation and other technologies the way integrated circuits and microelectronics did 50-60 years ago,” Jain explained in an email. The goal is to “construct optical circuits of single crystal waveguides in a glass platform.”

Musterman’s work “showed details of these optical elements made in glass by a laser,” he added.

Jain, who is an alumnus of BNL, indicated that his lab is continuing to pursue the research Musterman started, with his former graduate student as a collaborator and guide.

Musterman appreciates the opportunity to work with other scientists from different academic and geographic backgrounds. In addition to working with other scientists and helping to refine the functionality of the SRX beamline, he plans to continue glass and glass crystallization research and their interactions with lasers. As he refines techniques, he hopes to answer questions such as measuring strain.

As glass is heated, atoms form an ordered crystalline arrangement that begins to grow. The nucleation event and crystal growth occurs at the atomic scale, which makes it difficult to observe experimentally. Nucleation is also rare enough to make it difficult to simulate.

Most theories describe crystal nucleation and growth in aggregate, leaving several questions unanswered about these processes on single crystals, Musterman explained.

As they are for most material processing, temperature and time are the most important factors for glass formation and glass crystallization.

Historically, studies of glass structure started shortly after the discovery of x-ray diffraction in 1913. In the 1950’s, S. Donald Stookey at Corning discovered he could crystallize glass materials to improve properties such as fracture resistance, which led to a new field of studies. Laser induced single crystal formation is one of the more recent developments.

Musterman and his colleagues found that laser crystallization does not always produce the same phase as bulk crystallization, although this is an active area of research.

Musterman created videos of the earliest stages of crystal growth under laser irradiation by direct imaging and with electron and x-ray diffraction.

Kiss anticipates that Musterman, who is reporting to him, will build infrastructure and understanding of the detection system in the first year, which includes building scanning routines to ensure that they know how to collect and interpret the data.

Once Musterman demonstrates this proficiency, the beamline scientists believe this expanded technical ability will interest scientists in several fields, such as materials science, energy science, Earth and environmental science and art conservation.

Pitching in with former colleagues

While Musterman is not required to work with other beamline users, he has helped some of his former colleagues at Lehigh as they “try to get their best data,” he said. He has also spoken with a scientist at Stony Brook University who has been collecting diffraction data.

A native of Troy, Missouri, Musterman lives in an apartment in Coram. When he was younger, he said science appealed to him because he was “always curious about how things worked.” He said he frequently pestered his parents with questions.

His father John, who owns a metal fabrication and machining business, would take various ingredients from the kitchen and encourage his son to mix them to see what happened. 

As for the future, Musterman would like to work longer term in a lab like Brookhaven National Laboratory or in industrial research.

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Jin Koda and Amanda Lee at the recent 243rd annual meeting of the American Astronomical Society in New Orleans. Photo by Jenny Zhang

By Daniel Dunaief

Hollywood is not the only place fascinated with the birth of stars. Indeed, researchers at Stony Brook University, among many other academic institutions, have focused considerable time, energy and effort into understanding the processes that lead to the creation of stars.

Astronomers had tried, unsuccessfully, to detect molecular clouds in the galaxy outskirts, which is how stars form in the inner part of galaxies.

About 18 years ago, a NASA satellite called GALEX discovered numerous newly formed stars at the edges of a spiral galaxy M83, which is 15 million light years from Earth. 

Leading an international team of scientists, Jin Koda, Professor in the Department of Physics and Astronomy at Stony Brook University, together with his former undergraduate student Amanda Lee, put together data and information from a host of sources to describe how these stars on the outer edge of the galaxy formed.

Their work demonstrated star-forming molecular clouds in this outer area for the first time.

“These molecular clouds at the galaxy edge are forming stars as much as the molecular clouds in normal parts of galaxies” such as molecular clouds around the sun, Koda explained.

Before their discovery, Koda said astronomers had considered that new-born stars at galaxy edges could have formed without molecular clouds.

Koda recently presented this work at the 243rd annual meeting of the American Astronomical Society in New Orleans.

Indeed, partnering with scientists from the United States, Japan, France and Chile, Koda, who is the Principal Investigator on the study, and Lee found evidence of 23 of these molecular clouds on the outskirts of the M83 galaxy.

Combining data from a host of telescopes for this research, Koda and Lee found “higher resolution than before,” Lee said. “We could see a peak of atomic hydrogen in that region, which we didn’t know before.”

While helium also exists in the molecular clouds in the galaxy edges as well as in the atomic gas and in stars, it does not emit light when it’s cold, which makes its signature harder to detect.

Scientists are interested in “why we weren’t able to detect these molecular clouds for such a long time,” Lee said. “We ended up using a different tracer than what is normally used.”

The group came up with a hypothesis for why the molecular clouds were difficult to find. Carbon monoxide, which typically helps in the search for such clouds, is dissociated in the large envelopes at the galaxy edges. Only the cores maintain and emit this gas.

A collaboration begins

When Lee, who grew up in Queens, started at Stony Brook University, she intended to major in physics. In her sophomore year, she took an astronomy class that Koda taught.

“I was very interested in studying galaxies and the evolution of galaxies,” Lee said.

After the course ended, she started working in Koda’s lab.

“Her tireless efforts made her stand out,” Koda explained in an email. Koda appreciates how speaking with students like Lee helps him think about his research results.

Lee is “particularly good at identifying and asking very fundamental questions,” he added.

At one point about two years before she graduated in 2022, Lee recalled how Koda shared a picture of M83 and described the mystery of star formation at the outskirts of galaxies.

Two years later, by delving into the data under Koda’s supervision, she helped solve that mystery.

“I didn’t know my work would end up contributing to this project,” Lee said. “It’s really exciting that I was able to contribute to the big picture of star formation” in distant galaxies.

Since graduating from Stony Brook, Lee has been a PhD student for the last year and a half at the University of Massachusetts at Amherst.

At this point, Lee is still working towards publishing a paper on some of the work she did in Koda’s lab that explores the formation of stars in the inner disk of M83.

“Broadly,” she said, the two research efforts are “all related to the same picture.”

For her part, Lee was pleased with the opportunity to work with such a geographically diverse team who are all contributing to the goal of understanding star formation.

Future focus

The area they observed is relatively small and they would like to see more regions in M83 and other galaxies, Koda explained.

Finding so many molecular clouds at once in the small region “encourages us to hypothesize that the process is universal,” although scientists need to verify this, Koda said.

The researchers also discovered more atomic gas than they would expect for the amount of molecular clouds. A compelling discovery, this observation raised questions about why this abundant atomic gas wasn’t becoming molecular clouds efficiently.

“We need to solve this mystery in future research,” Koda explained. He is pleased with the level of collaboration among the scientists. “It’s very interesting and stimulating to collaborate with the excellent people of the world,” he said.

A resident of Huntington, Koda grew up in Tokyo, where he earned his bachelor’s, master’s and PhD degrees. When he moved to the United States, Koda conducted post doctoral studies for six years at Cal Tech. 

About 15 years ago, he moved to Stony Brook, where he replaced Professor Phil Solomon, who was one of the pioneers of molecular cloud studies in the Milky Way galaxy.

Science appeals to Koda because he is “interested in how things work, especially how nature works,” he said.

In this work, Koda suggested that the molecular clouds have the same mass distribution as molecular clouds in the Milky Way, indicating that star formation is the same, or at least similar, between the Milky Way and galaxy edges.

Koda made the discovery of the molecular clouds and the hypothesis about the carbon monoxide deficient cloud envelope in 2022. Since then, he and his team have obtained new observations that confirmed that what they found were the “hearts of molecular clouds,” he said.

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Pixabay photo

By Daniel Dunaief

Daniel Dunaief

Some historical phrases help shape and define the country the way landmarks like the Grand Canyon, Statue of Liberty, and Mt. Rushmore provide a distinct national identity.

One of those expressions, for me, is “rugged individualism.” The combination of the two words suggest independent thought, an ability to decide for ourselves, and a willingness to eschew tradition in favor of something more personal, practical and self-directed.

We don’t need kings and monarchs to tell us how to behave or to dictate from on high. We favor the stories of Americans whose humble origins offered hope to anyone born in a log cabin, a la Abraham Lincoln, or whose compassion inspired them to build houses for others, Jimmy Carter, perhaps, long after they were no longer the most powerful person on the planet.

We think for ourselves, we live with the view that we have unlimited potential and that we don’t need to have the right name or address to realize our dreams. Our self confidence allows us to imagine that we can become the next “Cinderella Man” or “Working Girl.”

And yet, we the people of the United States sometimes appear to be living lives that are filled with paint-by-the-numbers decisions and that involve following other people’s footprints in the snow.

Why? Have we and our children become so accustomed to group think that we don’t want to separate ourselves from the pack? Are we living in a world where we are desperate to conform?

Part of our collapse in independent thinking comes from corporate America. That faceless, nameless, profit churning machine, with its fake wooden boardrooms and its army of handlers and focus groups, has encouraged us to believe that buying their products, supporting their stores and following the trends is a way of asserting our independence.

It’s a clever ploy, my friends. They convince you that eating what everyone else eats, saying the same words everyone else says and wearing what everyone else wears helps you realize your potential.

The argument is an easy one to make, especially as you drive through Anytown USA. You see the same collection of franchised stores, with their predictable food and products and their well-oiled experiences, where it takes 5.6 minutes from the time you entered the store to get exactly the same soggy french fries in Dubuque, Iowa as it would in Setauket, New York.

We resist risk. Going into a restaurant with an unknown name means we might consume food that doesn’t taste familiar or good to us and that might give us indigestion as we move, like cattle, to the next predictable destination and engage in an echo of the same conversation we had last week, last month and last year.

I get it: it’s hard to decide to go to a unique store or restaurant in a town, particularly when the parking lot in the franchise chain next door is packed with people driving the same model and color cars we see on our roads back home.

Well, it’s 2024, and not 1984. We can and should make our own decisions. I would encourage you, your children and your friends to decide who you are and what that means. Yes, it’s hard and yes, people might hide behind the cloak of conformity to encourage you to do as they and everyone else does. They might even peck at you verbally, uncomfortable with differences and unsure of how to react to “the real you.”

If we fit in too well everywhere we go, we run the risk of disappearing. As Frank Sinatra suggests, it’s time to do things “My Way.” Yes, we might hate tuna fish with peanut butter, but at least we’ll be listening to our own voice and getting off a nonstop conveyor belt of conventional thought in which we follow the same roads, the same thoughts, and the same routines. Different? Different is good and, best of all, it’s up to you to decide what that means.

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James Konopka. Photo by Susan Watanabe

By Daniel Dunaief

Most of the time, the fungus Candida albicans, which is ubiquitous on the skin, inside people’s mouths, throat, and guts, among other places, doesn’t cause problems. It can, however, be an opportunistic infection, particularly in people who are immunocompromised, leading to serious illness and even death.

Antifungal infections work best during the early stage of an infection. Once a severe infection becomes established, it responds less well to drugs, as resistance can become a problem.

James “Jamie” Konopka, Professor in the Department of Microbiology and Immunology in the Renaissance School of Medicine at Stony Brook University, is working to find the mechanism that enables C. albicans to resist attack by the immune system. His long term goal is to identify ways to make the fungus more vulnerable to immune defenses.

In a paper published recently in the journal mBio, which is published by the American Society of Microbiology, Konopka identified the mechanism by which hypochlorous acid, which is produced by cells in the immune system, attacks C. albicans.

He expanded this by testing forms of the fungus that lack specific genes. These mutants can be more vulnerable to attack by hypochlorous acid, which is produced by neutrophils and is also called “human bleach.” Longer term, Konopka hopes to find ways to sensitize the fungus to this acid, which would bolster the ability of the immune system to respond to an infection.

His study showed that hypochlorous acid disrupts the plasma membrane, which is a layer of lipids that surround the cell. Once this is breached, parts of the cell leak out, while more bleach can damage the fungus.

Hypochlorous acid reacts with proteins, lipids and DNA.

The activated immune system produces several chemicals known as “reactive oxygen species.” In some cells, particularly neutrophils, hydrogen peroxide is converted into hypochlorous acid to strengthen and diversify the attack.

To be sure, the discovery of the mechanism of action of hypochlorous acid won’t lead to an immediate alternative therapeutic option, as researchers need to build on this study.

Future studies will examine how some genes promote resistance, and which are likely to be the most promising targets for drug development, Konopka explained.

Increase sensitivity

These are C. albicans cells growing invasively into tissue in a mouse model of an oral infection. The candida hyphae are stained black, and the tissue is stained a blue/green. Image from James Konopka

Konopka suggested that increasing the sensitivity of the fungus to hypochlorous acid would likely prove more effective and less potentially toxic than increasing the amount of the acid, which could also damage surrounding tissue.

“Our idea is to sensitize fungal pathogens” to hypochlorous acid “rather than upping the dose of bleach, which could lead to negative consequences,” Konopka said. Ideally, he’d like to “take the normal level and make it more effective” in eradicating the fungus.

Other scientists funded by the National Institutes of Health created a set of about 1,000 different strains of the fungus, which provides a valuable resource for Konopka and others in the scientific community.

In a preliminary screen of plasma membrane proteins, Konopka and his team found that most of the mutants had at least a small increase in sensitivity. Some, however, had stronger effects, which will guide future experiments.

One of the challenges in working with a fungus over pathogens like bacteria or viruses is that fungi are more closely related biologically to humans. That means that an approach that might weaken a fungus could have unintended and problematic consequences for a patient.

“Although they may look very different on the outside, the inner workings of fungi and humans are remarkably similar,” Konopka explained in an email. This has made it difficult to find antifungal drugs that are not toxic to humans.

An ‘overlooked’ ally

Konopka suggested that scientists have been studying hydrogen peroxide, which is also made by immune system combatants like macrophages and neutrophils.

“It seemed to us that somehow bleach had been overlooked,” Konopka said. “It hadn’t been studied in the fungal world, so we launched” their research.

Konopka also believes the plasma membrane represents an effective place to focus his efforts on developing new drugs or for making current drugs more effective. 

Hydrochlorous acid “fell into our wheel house,” he said. In initial tests, Konopka discovered that human bleach caused damage to the membrane within minutes if not sooner, allowing outside molecules to enter freely, which could kill the potentially dangerous infection.

Considering the ubiquitous presence of the fungus, immunocompromised people who might conquer an infection at any given time could still be vulnerable to a future attack, even after an effective treatment. Even people with a healthy immune system could be reinfected amid a large enough fungal load from a biofilm on a medical device or catheter.

Providing vulnerable people with a prophylactic treatment could lower the risk of infection. When and if those patients develop an ongoing and health-threatening infection, doctors could use another set of drugs, although such options don’t currently exist.

In other work, Konopka has identified proteins in C. albicans that help CoQ, or ubiquinone, protect the plasma membrane from oxidation by agents such as hydrogen peroxide and hypochlorous acid.

People can purchase ubiquinone at local stores, although Konopka urges residents to check with their doctors before taking any supplement.

Fish and beer

An organizer of a department wide Oktoberfest, Konopka was pleased that faculty, post doctoral researchers and students were able to decompress and enjoy the fall festival together for the first time since 2019.

In addition to a range of beer, attendees at the event, which occurred half way between the start of the semester and final exams, were able to partake in German food from Schnitzels in Stony Brook Village, which was a big hit.

An avid fly fisherman who catches and releases fish, Konopka said he caught some bigger striped bass this year than in previous years.

When he’s fishing, Konopka appreciates the way the natural world is interconnected. He pays attention to variables like the weather, water temperature, bait fish and the phases of the moon.

He particularly enjoys the wind and fresh air. This year, Konopka marveled at the sight of a bald eagle.

As for his work, Konopka said basic research may have an immediate effect or may contribute longer term to helping others in the scientific community build on his results, which could lead to the next breakthrough.

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Pixabay photo

By Daniel Dunaief

Daniel Dunaief

The reality of aging is that we sometimes wake up feeling like we’ve got less than a full tank of gas, or, for those of you driving electric vehicles, a fully charged battery, with which to maneuver through the day.

Maybe our ankles are sore from the moment we imagined we could still dive across the grass to catch a foul ball. Perhaps, less ambitiously, we twisted our ankle when we took a bad step on a sidewalk as we did something much less heroic, like texting an old friend or playing a mindless video game. Or it hurts because it, like our jobs, our cars, and our homes, inexplicably needs attention.

What’s the antidote to the numerous headwinds that slow us down and make us feel exhausted earlier each day?

The start of a new year can provide that energy and inspiration. We get to write 2024 on our checks, if we’re still writing them, we can imagine a blank canvas on which we can reinvent ourselves, find new friends, get new jobs, travel to new places, live our values and contribute meaningfully to the world.

We can start jotting activities into that new calendar, smiling as we imagine seeing friends we haven’t seen in years or decades or fulfilling long-held desires to shape our lives, our bodies or both into what we’ve always imagined.

On a more immediate scale, we have other ways to boost our energy. We can grab a steaming hot cup of hot chocolate or coffee, loading our nervous system up with caffeine, which can wake us up and help us power through the next few hours.

We can also grab a donut, a cookie, or some other food loaded with sugar, knowing, of course, that we run the risk of emptying that short-energy tank quickly after the sugar rush ends.

I have discovered plenty of places I can go, literally and figuratively, to feel energized and inspired. My list includes:

Our children: Yes, they are draining and can be demanding and needy, but their youth and energy can be restorative. They take us to places we hadn’t been before, give us an opportunity to share books we might have missed in our own education and offer insights about themselves and their world that amaze us. Their different interests and thoughts keep us on our toes, focused and, yes, young, as we try to meet them where they live. As we relate to them, we can also imagine our own lives at that age.

Our pets: Watching a dog chase a ball, its tail or a frisbee, or observing a cat push a ball of string across the floor can be invigorating. If we threw that ball or tossed that string, we become a human partner in their games, giving us a role to play even as they expend considerably more effort in this entertaining exchange.

Nature: Energy surrounds us. Water lapping on the shores of Long Island at any time of year, small leaf buds responding to the cues of spring, and birds calling to each other through the trees can inspire us and help us feel alert, alive and aware of the symphony of life that serenades us and that invites us to participate in the evolving narrative around us.

Science: I have the incredible privilege of speaking with scientists almost every day. Listening to them discuss their work, when they don’t travel down a jargon rabbit hole filled with uncommon acronyms, is inspirational. The insatiable curiosity of scientists at any age  and any stage of their careers makes each discovery a new beginning. Each of their answers raises new questions. Scientists are always on the verge of the next hypothesis, the next great idea and the next adventure. Their energy, dedication and unquenchable thirst for knowledge invites listeners to participate in the next chapter in the evolving knowledge story.

Sunrises: Okay, if you’ve read this column often enough, you know I’m a morning person. I try to be quiet in the morning, for my family and for anyone else who stayed up late into the night. Sunrises, however, bring a welcome introduction to something new and original.

History: reading about or studying history puts our world into perspective. We not only can contrast previous time periods with today, but we also can enjoy and appreciate that we have the opportunity to share in and shape this moment.

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Dima Kozakov. Photo from SBU
Michael Zingale. Photo by John Griffin/SBU

By Daniel Dunaief

They have little in common. One studies deep inside cells to understand the difference between diseased and healthy states. The other explores models that represent distant thermonuclear reactions.

What Stony Brook University’s Dima Kozakov, Professor in the Department of Applied Mathematics and Statistics, and Michael Zingale, Professor in the Department of Physics and Astronomy, share, however, is that both led teams that recently won a Department of Energy grant that will allow them to use the fastest publicly available supercomputer in the world, at DOE’s Oak Argonne and Oak Ridge National Laboratories.

Kozakov and Zingale, who are both members of the Institute for Advanced Computational Sciences, are recipients of the DOE’s grants through its Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program.

“It’s a huge recognition of computation” not just at the IACS, but also for Stony Brook in general, said Robert Harrison, Director of the IACS and Professor in the Department of Mathematics & Statistics. Kozakov and Zingale are the “point persons on world-class teams [which] positions Stony Brook at the forefront of the scientific community.”

Harrison suggested that the astrophysics group at Stony Brook was already world class when he arrived a decade ago and the university has been pushing to move Stony Brook to take advantage of all the modern powerful tools for simulation and data driven discovery.

Disease states

Kozakov, who is also an affiliate of the Laufer Center for Physical and Quantitative Biology,  plans to model enormous numbers of molecular interactions to compare how they function in diseased cells with how they work in healthy cells.

He and his team will get the data on important proteins and interactions in disease compared with healthy cells from high throughput but noisy experiments and validate those computationally.

By studying diseases such as cancer, diabetes and Alzheimer’s, Kozakov plans to look for clues about what occurs at the level of the atomic structure of protein interactions, hoping such an analysis points to the creation of new types of therapies.

Kozakov will use a combination of publicly available data and information from some of his experimental collaborators to identify new targets that small molecules may alter amid a diseased state. He feels the tight integration between the theoretical and the experimental nature of the team will enhance its effectiveness.

A supercomputer “allows you to try many approaches in parallel” such as training deep learning models that require trying many options to get the best possible ones, he said.

The pilot work the team has done created the kind of momentum that increased the chance of securing funds and time through the INCITE program.

Kozakov and co-investigators including Assistant Professor Pawel Polak at Stony Brook, Professor Andrew Emili at OHSU, Associate Professor Matthew Torres at Georgia Tech and Julie Mitchell, the Director of Biosciences Division at Oak Ridge National Laboratory, were “very happy” when they learned they’d won the award. he said. “It’s good to know that people appreciate the [work] we are doing.”

Starry, starry explosion

In the meantime, Zingale’s project, called “Exascale Models of Astrophysical Thermonuclear Explosions,” was renewed for a second year in the INCITE program.

Zingale leads a team that explores two types of astrophysical thermonuclear explosions to understand these physical processes and their broader implications. The computational work is focused mostly on whether a particular model for a thermonuclear explosion is viable.

“We really want to just understand: does it explode or not?” Zingale explained. His work focuses on the explosion mechanism and on the design of algorithms that can efficiently model these explosions.

Graduate students Zhi Chen, Alexander Smith Clark, Eric Johnson, Melissa Rasmussen, and Khanak Bhargava will be working with the supercomputer in the next year, Zingale added.

“Each student is working on separate questions, both on this problem and on related problems (novae and x-ray bursts),” said Zingale. “The goals are the same — in each case, we want to produce a realistic model of the burning that takes place in these events to understand how these explosions unfold.”

Models help connect to the observations astronomers make. While the work doesn’t produce new physics, it allows researchers to gain a greater understanding of supernovae.

Numerous other groups around the world are pursuing similar simulations, which Zingale explained is favorable for the science.

“If we all get the same result using different codes and techniques, then it gives us confidence that we might be understanding what is actually taking place in nature,” he said.

The explosions Zingale is studying differ from those on Earth because they are far larger and can reach higher densities in stars, which produces elements up to iron in explosions. The tools he uses to model these explosions have “similarities to the techniques used to model chemical combustion on Earth,” he said. “We work with applied mathematicians that study terrestrial flames and can use the techniques” in the astrophysical setting.

Zingale explained that he was always interested in astronomy and computers, so this field of work serves as the bridge between the two.

For students interested in the field, Zingale added that it teaches people how to solve complex problems on computers.

“Even if you don’t stay in the field, you build skills that are transferable to industry (which is where many of my graduate students wind up),” he said. He urges people to study something they enjoy. The main code he uses is called Castro and is freely available online, which means that “anyone can look at what we’ve done and run it for themselves,” he explained.

Student opportunities

For Stony Brook graduate students, these INCITE awards offer opportunities for additional learning and career advancement.

“The excitement is infectious,” said Harrison. “The students see not just the possibility to be at the frontier of discovery and the frontier of technology [but also to have] the career opportunities that lie beyond that.”

Students trained to make effective use of these platforms of cutting-edge science are “heavily recruited, going into industry, national labs, working for the likes of Google and so on,” Harrison added.

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METRO photo

By Daniel Dunaief

Daniel Dunaief

Here we are, poised on the precipice of 2024, or, if you’d prefer, at the bottom of the mountain, looking up at the year ahead.

What a privilege to start 2024 together, to share the same air, to enjoy or brace for the same weather, to root for or against the same teams and to revel in the miracle of our children, grandchildren, nieces, nephews and neighbors.

As we venture into the days, weeks and months ahead, we can all see certain patterns continuing because, let’s face it, we know the familiar playbook people use. I would love to figure out how to capitalize on some coming certainties. If, for example, we had a dime for every time the song “Jingle Bells” came on in department stores around the country in the last few weeks of each year, we’d have enough money to buy our own one-horse open sleigh and fill it with presents. With that in mind, I’d like to consider certainties or near certainties in various realms.

Political:

Let’s start with former president Donald Trump. A dime for every time he insulted someone could pay for an enjoyable and deluxe vacation to Europe or, if you prefer, a week or more at a Disney resort.

A dime for each time he uttered the words “rigged,” “witch hunt,” or “socialist,” would also net some nice cash.

Collecting money when he referred to himself in the third person, as in “only Donald Trump can fix that” would also prove profitable.

President Biden, of course, has his go-to approaches and idiosyncrasies as well. Collecting money when he misspoke or stepped in the wrong direction would turn gaffes into cash.

Or, perhaps, adding money each time he became angry or annoyed with someone would also provide considerably more change than the typical back of the couch.

Collecting cash each day that goes by without the president taking questions from the Press Corps or reacting to unscripted moments would also build wealth.

A dime for each time Chris Christie insults Trump would help build a college fund.

Oh, and some change for each time Jim Jordan (R-OH) takes off his coat, MTG scowls, Ron DeSantis uses the word “woke” or attacks Disney, AOC insults NYC, or Nikki Haley smiles when she’s insulted would also make real money.

Sports:

Ah, yes, the world of sports not only is filled with cliches, but also has predictable patterns.

Fans and sports talk radio hosts always know better. Monday morning quarterbacking has become something between a religion and a profession.

The next day, everyone else always claims to have known exactly when to take a pitcher out of a ballgame, when to run the ball and when to take a time out. 

The pundits on the sidelines always know better about the Big Game than the people who are paid to make the decisions.

And, of course, with the Olympics coming in Paris this year, we can anticipate the back stories about athletes who are competing in memory of a cherished dead relative who inspired them. If we the viewers had a dime for every tear shed during these serious and melodramatic moments, we’d be able to afford the plane ticket to Paris to watch the Games in person.

I’m not minimizing the inspiration these athletes take from their relatives, coaches and friends. I’m reflecting on the types of stories, with their sad, moving slow guitar background music, these networks share, combining loss and grief with determination and the quest for glory.

Random but predictable moments:

As a coach for many teams, I am sure parents throughout the country are convinced that their children are being short changed. A dime for each parent complaint could provide a down payment for a new field.

I’d also like to collect money each time someone who talks all the time “breaks their silence” on something. It’s amusing when headline writers suggest that, say, Britney Spears or one of the Kardashians breaks their silence on anything. I thought these non-stop celebrities shared every thought in their heads. Ah yes, a dime for each deep internal secret of people who would do well to be more discrete would also build wealth.

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